When Paul Stephenson stepped into the role of Scotland Yard commissioner as successor to Sir Ian Blair he was clear on one thing. Unlike Blair, he would not become the story. He would be, he was proud to admit, the boring one.

It was the Met, the work of its detectives, its uniformed officers and its ability to cut crime that would, he said, make the headlines.

That he has managed to fulfil that for two and a half years is a credit to his determination to stay out of the spotlight. He has overseen a fall in crime to a 10-year low, a reduction in gun crime and a fall in homicide.

That he has resigned after becoming so publicly part of the extraordinary fallout of the phone-hacking affair and its impact on the Murdoch empire is an irony he will not enjoy.

Only recently, following criticism in the Metropolitan police authority of the amount of resources being used on Operation Weeting, Stephenson said that the detectives involved would go wherever the evidence led them. He cannot have imagined being part of their collateral damage.

Following Stephenson's departure, questions will surely be raised about his right-hand man, Dick Fedorcio, the Met's director of public affairs and internal communication, who has guided and advised him.

There will also be more pressure on assistant commissioner John Yates, who has enjoyed Stephenson's support throughout the unravelling of the phone hacking scandal.

It is perhaps extraordinary that of everyone allegedly involved in the phone hacking saga, it is Stephenson who has gone – and unlike many involved, has had the honour to go without a long, drawn-out delay damaging his organisation.

What may now emerge is what many within the Met called for after Sir Ian Blair quit in October 2008 – fresh blood at the top of the organisation. Had that fresh blood been brought in by 2008 in the form of Sir Hugh Orde or Bernard Hogan-Howe – both Met men but out of the Yard for some time, the cozy and unchallenged clique at the top of Scotland Yard may have been shaken up and any unhealthy outside relationships with them.

Stephenson was the man chosen by Mayor Boris Johnson because, many said, he would not rock the boat and would quietly get on with the job after a period of turmoil under Blair. Stephenson had been chief constable of the Lancashire constabulary before joining the Met. He was popular with rank and file officers and robust when crossed.

Throughout his short tenure he has born personal tragedy. His daughter's fiance was killed in a road accident and the personal fall out for his whole family has been immense.

As with all commissionerships, there has been controversy. As acting commissioner he presided over the controversial arrest of Damian Green, the Conservative MP and, in the aftermath, his head of counter terrorism, Bob Quick, resigned. But to have to leave because of something he professes no involvement with, will be hard for him to swallow.

In his statement he denies knowledge of the Met's hiring of former News International executive Neil Wallis. That statement calls phone hacking "this disgraceful practice" and speaks of "the repugnant nature of the selection of victims that is now emerging".

With the Olympics one year away, the loss of Stephenson will be not just a personal blow for the man but a massive challenge to the organisation of the 2012 Games in London.

His successor must now come from outside; Sara Thornton of Thames Valley, Bernard Hogan-Howe at Her Majesty's Inspectorate of Constabulary, Sir Hugh Orde or Sir Norman Bettison. And their appointment will have to be swift.